scholarly journals In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Yang ◽  
Xiaohui Liu ◽  
Chengpin Shen ◽  
Yu Lin ◽  
Pengyuan Yang ◽  
...  
Keyword(s):  
Deep Learning ◽  
In Silico ◽  
State Of The Art ◽  
Protein Detection ◽  
Serum Samples ◽  
Data Independent Acquisition ◽  
Peptide Detectability ◽  
Spectral Libraries ◽  
Prediction In Silico

AbstractData-independent acquisition (DIA) is an emerging technology for quantitative proteomic analysis of large cohorts of samples. However, sample-specific spectral libraries built by data-dependent acquisition (DDA) experiments are required prior to DIA analysis, which is time-consuming and limits the identification/quantification by DIA to the peptides identified by DDA. Herein, we propose DeepDIA, a deep learning-based approach to generate in silico spectral libraries for DIA analysis. We demonstrate that the quality of in silico libraries predicted by instrument-specific models using DeepDIA is comparable to that of experimental libraries, and outperforms libraries generated by global models. With peptide detectability prediction, in silico libraries can be built directly from protein sequence databases. We further illustrate that DeepDIA can break through the limitation of DDA on peptide/protein detection, and enhance DIA analysis on human serum samples compared to the state-of-the-art protocol using a DDA library. We expect this work expanding the toolbox for DIA proteomics.

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Ferdinand Filip ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
State Of The Art ◽  
Science Methods ◽  
Learning Models ◽  
Diverse Range ◽  
Hybrid Machine ◽  
Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Data Science ◽  
State Of The Art ◽  
Hybrid Models ◽  
The Other ◽  
Learning Models ◽  
Comprehensive Review

Abstract This paper provides the state of the art of data science in economics. Through a novel taxonomy of applications and methods advances in data science are investigated. The data science advances are investigated in three individual classes of deep learning models, ensemble models, and hybrid models. Application domains include stock market, marketing, E-commerce, corporate banking, and cryptocurrency. Prisma method, a systematic literature review methodology is used to ensure the quality of the survey. The findings revealed that the trends are on advancement of hybrid models as more than 51% of the reviewed articles applied hybrid model. On the other hand, it is found that based on the RMSE accuracy metric, hybrid models had higher prediction accuracy than other algorithms. While it is expected the trends go toward the advancements of deep learning models.

scholarly journals Deep learning for brain disorders: from data processing to disease treatment

2020 ◽  
Author(s):  
Ninon Burgos ◽  
Simona Bottani ◽  
Johann Faouzi ◽  
Elina Thibeau-Sutre ◽  
Olivier Colliot
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Language Processing ◽  
State Of The Art ◽  
Imaging Genetics ◽  
Environmental Data ◽  
Brain Disorders ◽  
Disease Treatment ◽  
Clinical Routine

Abstract In order to reach precision medicine and improve patients’ quality of life, machine learning is increasingly used in medicine. Brain disorders are often complex and heterogeneous, and several modalities such as demographic, clinical, imaging, genetics and environmental data have been studied to improve their understanding. Deep learning, a subpart of machine learning, provides complex algorithms that can learn from such various data. It has become state of the art in numerous fields, including computer vision and natural language processing, and is also growingly applied in medicine. In this article, we review the use of deep learning for brain disorders. More specifically, we identify the main applications, the concerned disorders and the types of architectures and data used. Finally, we provide guidelines to bridge the gap between research studies and clinical routine.

scholarly journals DLNR-SIQA: Deep Learning-Based No-Reference Stitched Image Quality Assessment

Sensors ◽  
2020 ◽  
Vol 20 (22) ◽  
pp. 6457
Author(s):  
Hayat Ullah ◽  
Muhammad Irfan ◽  
Kyungjin Han ◽  
Jong Weon Lee
Keyword(s):  
Deep Learning ◽  
Image Quality ◽  
Quality Assessment ◽  
Image Quality Assessment ◽  
State Of The Art ◽  
Reference Image ◽  
Primary Concern ◽  
Panoramic Images ◽  
Stitching Errors

Due to recent advancements in virtual reality (VR) and augmented reality (AR), the demand for high quality immersive contents is a primary concern for production companies and consumers. Similarly, the topical record-breaking performance of deep learning in various domains of artificial intelligence has extended the attention of researchers to contribute to different fields of computer vision. To ensure the quality of immersive media contents using these advanced deep learning technologies, several learning based Stitched Image Quality Assessment methods have been proposed with reasonable performances. However, these methods are unable to localize, segment, and extract the stitching errors in panoramic images. Further, these methods used computationally complex procedures for quality assessment of panoramic images. With these motivations, in this paper, we propose a novel three-fold Deep Learning based No-Reference Stitched Image Quality Assessment (DLNR-SIQA) approach to evaluate the quality of immersive contents. In the first fold, we fined-tuned the state-of-the-art Mask R-CNN (Regional Convolutional Neural Network) on manually annotated various stitching error-based cropped images from the two publicly available datasets. In the second fold, we segment and localize various stitching errors present in the immersive contents. Finally, based on the distorted regions present in the immersive contents, we measured the overall quality of the stitched images. Unlike existing methods that only measure the quality of the images using deep features, our proposed method can efficiently segment and localize stitching errors and estimate the image quality by investigating segmented regions. We also carried out extensive qualitative and quantitative comparison with full reference image quality assessment (FR-IQA) and no reference image quality assessment (NR-IQA) on two publicly available datasets, where the proposed system outperformed the existing state-of-the-art techniques.

scholarly journals GproDIA enables data-independent acquisition glycoproteomics with comprehensive statistical control

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yi Yang ◽  
Guoquan Yan ◽  
Siyuan Kong ◽  
Mengxi Wu ◽  
Pengyuan Yang ◽  
...  
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Statistical Control ◽  
Serum Samples ◽  
Accurate Identification ◽  
Spectrum Prediction ◽  
Data Independent Acquisition ◽  
Stage Of Development ◽  
Spectral Libraries ◽  
Semi Empirical

AbstractLarge-scale profiling of intact glycopeptides is critical but challenging in glycoproteomics. Data independent acquisition (DIA) is an emerging technology with deep proteome coverage and accurate quantitative capability in proteomics studies, but is still in the early stage of development in the field of glycoproteomics. We propose GproDIA, a framework for the proteome-wide characterization of intact glycopeptides from DIA data with comprehensive statistical control by a 2-dimentional false discovery rate approach and a glycoform inference algorithm, enabling accurate identification of intact glycopeptides using wide isolation windows. We further utilize a semi-empirical spectrum prediction strategy to expand the coverage of spectral libraries of glycopeptides. We benchmark our method for N-glycopeptide profiling on DIA data of yeast and human serum samples, demonstrating that DIA with GproDIA outperforms the data-dependent acquisition-based methods for glycoproteomics in terms of capacity and data completeness of identification, as well as accuracy and precision of quantification. We expect that this work can provide a powerful tool for glycoproteomic studies.

scholarly journals DIAFree enables untargeted open-search identification for Data-Independent Acquisition data

2020 ◽  
Author(s):  
Iris Xu
Keyword(s):  
Data Processing ◽  
High Throughput ◽  
Protein Analysis ◽  
Processing Algorithm ◽  
Software Suite ◽  
Data Processing Algorithm ◽  
Link Type ◽  
Data Independent Acquisition ◽  
Spectral Libraries

AbstractAs a reliable and high-throughput proteomics strategy, data-independent acquisition (DIA) has shown great potential for protein analysis. However, DIA also imposes stress on the data processing algorithm by generating complex multiplexed spectra. Traditionally, DIA data is processed using spectral libraries refined from experiment histories, which requires stable experiment conditions and additional runs. Furthermore, scientists still need to use library-free tools to generate spectral libraries from additional runs. To lessen those burdens, here we present DIAFree(https://github.com/xuesu/DIAFree), a library-free, tag-index-based software suite that enables both restrict search and open search on DIA data using the information of MS1 scans in a precursor-centric and spectrum-centric style. We validate the quality of detection by publicly available data. We further evaluate the quality of spectral libraries produced by DIAFree.

scholarly journals Comparison of Attention-based Deep LearningModels for EEG Classification

2021 ◽  
Author(s):  
Giulia Cisotto ◽  
Alessio Zanga ◽  
Joanna Chlebus ◽  
Italo Zoppis ◽  
Sara Manzoni ◽  
...  
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Classification Performance ◽  
Classification Problems ◽  
Large Variability ◽  
Eeg Classification ◽  
Time Frequency ◽  
Promising Strategy ◽  
Complex Reasoning

Abstract Deep Learning (DL) has recently shown promising classification performance in Electroencephalography (EEG) in many different scenarios. However, the complex reasoning of such models often prevent the user to explain their classification abilities. Attention, one of the most recent and influential ideas in DL, allows the models to learn which portions of the data are relevant to the final classification output. In this work, we compared three attention-enhanced DL models, the brand-new InstaGATs , an LSTM with attention and a CNN with attention. We used these models to classify normal and abnormal, including artifactual and pathological, EEG patterns in three different datasets. We achieved the state of the art in all classification problems, regardless the large variability of the datasets and the simple architecture of the attention-enhanced models. Additionally, we proved that, depending on how the attention mechanism is applied and where the attention layer is located in the model, we can alternatively leverage the information contained in the time, frequency or space domain of the EEG dataset. Therefore, attention represents a promising strategy to evaluate the quality of the EEG information, and its relevance for classification, in different real-world scenarios.

scholarly journals Data Science in Economics: Comprehensive Review of Advanced Machine Learning and Deep Learning Methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Data Science ◽  
State Of The Art ◽  
Hybrid Models ◽  
The Other ◽  
Learning Models ◽  
Comprehensive Review

This paper provides the state of the art of data science in economics. Through a novel taxonomy of applications and methods advances in data science are investigated. The data science advances are investigated in three individual classes of deep learning models, ensemble models, and hybrid models. Application domains include stock market, marketing, E-commerce, corporate banking, and cryptocurrency. Prisma method, a systematic literature review methodology is used to ensure the quality of the survey. The findings revealed that the trends are on advancement of hybrid models as more than 51% of the reviewed articles applied hybrid model. On the other hand, it is found that based on the RMSE accuracy metric, hybrid models had higher prediction accuracy than other algorithms. While it is expected the trends go toward the advancements of deep learning models.

scholarly journals Data science in economics: comprehensive review of advanced machine learning and deep learning methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Ferdinand Filip ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
State Of The Art ◽  
Science Methods ◽  
Learning Models ◽  
Diverse Range ◽  
Hybrid Machine ◽  
Economics Research

This paper provides a state-of-the-art investigation of advances in data science in emerging economic applications. The analysis was performed on novel data science methods in four individual classes of deep learning models, hybrid deep learning models, hybrid machine learning, and ensemble models. Application domains include a wide and diverse range of economics research from the stock market, marketing, and e-commerce to corporate banking and cryptocurrency. Prisma method, a systematic literature review methodology, was used to ensure the quality of the survey. The findings reveal that the trends follow the advancement of hybrid models, which, based on the accuracy metric, outperform other learning algorithms. It is further expected that the trends will converge toward the advancements of sophisticated hybrid deep learning models.

DeepMSPeptide: peptide detectability prediction using deep learning

2019 ◽  
Author(s):  
Guillermo Serrano ◽  
Elizabeth Guruceaga ◽  
Victor Segura
Keyword(s):  
Deep Learning ◽  
Protein Detection ◽  
Amino Acid Sequences ◽  
Supplementary Information ◽  
Learning Method ◽  
Supplementary Data ◽  
Stochastic Nature ◽  
Bioinformatic Tool ◽  
Peptide Detectability ◽  
Detection And Quantification

Abstract Summary The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry, also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript, we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences. Availability and implementation DeepMSPeptide is available at https://github.com/vsegurar/DeepMSPeptide. Supplementary information Supplementary data are available at Bioinformatics online.

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